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PR 1 #160

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@anjag01 anjag01 commented May 4, 2025

Description

Checklist

  • Make sure that you are listed in the AUTHORS file
  • Add relevant changes and new features to the CHANGELOG file
  • I have commented my code, particularly in hard-to-understand areas
  • New and existing unit tests pass locally with my changes
  • Updated or added python bindings for changed or new classes (Tick if no updates were necessary.)

How can I get additional information on failed tests during CI

Click to expand If your PR is failing you can check out
  • The details of the action statuses at the end of the PR or the "Checks" tab.
  • http://cdash.seqan.de/index.php?project=OpenMS and look for your PR. Use the "Show filters" capability on the top right to search for your PR number.
    If you click in the column that lists the failed tests you will get detailed error messages.

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Click to expand
  • /reformat (experimental) applies the clang-format style changes as additional commit. Note: your branch must have a different name (e.g., yourrepo:feature/XYZ) than the receiving branch (e.g., OpenMS:develop). Otherwise, reformat fails to push.
  • setting the label "NoJenkins" will skip tests for this PR on jenkins (saves resources e.g., on edits that do not affect tests)
  • commenting with rebuild jenkins will retrigger Jenkins-based CI builds

⚠️ Note: Once you opened a PR try to minimize the number of pushes to it as every push will trigger CI (automated builds and test) and is rather heavy on our infrastructure (e.g., if several pushes per day are performed).

cbielow and others added 30 commits October 30, 2023 14:19
@cbielow
fix error in concatenation
3a3c006
@cbielow
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into develop
432955c
@cbielow
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into develop
0968e8e
@cbielow
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into develop
bc0eb68
@cbielow
make GaussFitter a lot faster
dd9fa42
@cbielow
Merge branch 'develop' of https://github.com/OpenMS/OpenMS into feat_…
a845b65 
…ppfast
@subCode321
changed implementation
94e59bd
@subCode321
Revert "changed implementation"
9be6e33 
This reverts commit 94e59bd.
@subCode321
add const and const iterator
0aaee0e
@subCode321
add logic to find minima
3043106
@subCode321
add min finder utility
4ebfa4c
@subCode321
Merge branch 'develop' into alignwork
f2ff27e
@subCode321
use getScoreComparator static const function
6230eb3
@subCode321
Merge branch 'alignwork' of github.com-subcode:subCode321/OpenMS into…
bdd798d 
… alignwork
@subCode321
document higher score better
4d72e81
@subCode321
test running after change
eecc3d7
@subCode321
rename param
82edd85
@subCode321
fix param docs
4e81515
@cbielow
Merge pull request OpenMS#7973 from subCode321/alignwork
cf1aed5 
Made align function work on const data
@t0mdavid-m
Enable OpenMP for pyOpenMS on MacOS (OpenMS#7980)
41ff5fb 
* add test run

* push on dev

* create contrib folder

* Delete .github/workflows/test_contrib.yml

* disable openmp for arm wheels

* set rpath

* try fix from abibuilder

* switch linking

* fix typo

* add print for libraries

* fix openmp build flags

* fix rpath in workflow

* dont remove source

* install wheels

* run unit test separately

* Revert "install wheels"

This reverts commit 7c159d2.

* Revert "run unit test separately"

This reverts commit 5b854cb.

* Reapply "install wheels"

This reverts commit 0f1ff8d.

* Revert "dont remove source"

This reverts commit 227b3a9.

* is brew libomp the issue?

* update rpath

* rpath to lib

* update cmake args

* remove lib

* move test files to tests

* move test files

* dont uninstall brew

* cleanup

* fix typo

* clean up libs

* cleanup
@timosachsenberg
refactor: move basename member out of PeptideIdentification into Meta…
cce935f 
…Values (OpenMS#7981)

* move basename member out of PeptideIdentification into MetaValues

* fix tests and simplify them

* remove base name (not needed)

* strange character fix
@timosachsenberg
doc: PeptideHit and PeptideIdentification (OpenMS#7983)
a2bb639 
* improve doc, add type alias

* Add deprecation notice for PeptideHit class

* Deprecate PeptideIdentification in favor of SpectrumIdentification
@poshul
Update THIRDPARTY and lay groundwork for linux ARM support (OpenMS#7811)
b9914d4 
* Add ubuntu arm to matrix

* Update thirdparty with new percolator and some arm64 stuff

* Update thirdparty, update Percolator version

* Update percolator test for 3.07 (NB the actual Percolator 3.07 release still uses 3.06 in their executable)

* Add logic to copy the correct THIRDPARTY executables for the current arch

* Update Comet versions in all OSs update comet test files for the new version.

* add status of copy

* cp issues for macZZ

* Update openms_ci_matrix_full.yml

Comment out the actual ARM run for now so we can merge the updated THIRDPARTY

* third
@timosachsenberg
type alias for MSexperiment (MSRun) (OpenMS#7988)
49cc1b4 
* reserve a type alias

* small additions to architecture file

* Documents manual Python extension capabilities

Adds a detailed section on using manual PYX files to extend Python bindings, covering advanced functionality such as handling complex C++ features, Python-specific enhancements, performance optimizations, and integration with Python libraries. Clarifies the role of PYX files in enabling features beyond automatic wrapping.

* Update ARCHITECTURE.MD
@timosachsenberg
refactor: move significance_threshold and pepXML analysis results mem…
0b98927 
…ber in PeptideIdentifications to a meta value as it is often unused (OpenMS#7985)

* improve doc, add type alias

* move pepxmlanalysis results into meta values to simplify datastructure

* move significant threshold to metavalue

* some fixes

* Merge remote-tracking branch 'origin' into openms-pr-5547

* more test updates

* more fixes

* don't write it twice

* tests works

* fix tests

* more test fixes

* nop
Deleted redundant test1.cpp
4ac5dc1
Deleted redundant test1.cpp
9777266
Deleted redundant test1.cpp
3619ecf
Deleted redundant test1.cpp
7471800
Deleted redundant test1.cpp
35f039e
Anjali Gajurel added 30 commits May 4, 2025 08:58
offsets specs and chroms
27e9db9
native id renewal
8d005c1
not empty offsets
fff6aa8
modified footer in handlerhelper and storeBuffer
3639eb2
storeBuffer tweaks
1b5b9c9
modified safeParse
9f05be9
MzMLFile1 -> MzMLFile_1 in test file
a5fc8b1
always store offsets
7349113
offsets and counter
a50bf29
writeTo tweaks
eb5f074
more tweaks
330993f
final changes
9227b48
debug output conditional in storBuffer
755f43b
reverted changes in storeBuffer, best_speed in boost
35cff7c
added the changes back
b73e774
header encoding in writeTo
64c04f3
revert
cff34c9
back to compression
92710e4
no validate in Classtest
b0d7f5a
pigz in writeTo from Nils, offsets when indexing enabled
a5e0ecc
pigz modification
8a44a7c
no opstream
7762e9e
modified pigz implementation
726fe57
pigz with boost::process::opstream
26d5734
pigz -c, build stopped
ff0c47b
pigz from Nils
dc031b8
max_threads
64ad509
forward declaration class basic_counter
0be3059
reverted changes in storeBuffer
36212b6
num_threads in writeTo
1a9011d
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8 participants
@anjag01 @cbielow @subCode321 @t0mdavid-m @timosachsenberg @poshul @pjones @jpfeuffer